[BioC] problem with combineAffyBatch

[Wolfgang Huber]

Hi Jared,

since the "combined" array is not really a physical array with x- and 
y-dimensions, the size information is meaningless.

Does the data rom the 1036 probe sets you get make sense?

Best wishes
  Wolfgang


Jared J. Bisogni wrote:
> Hello,
> I have been trying to combine data from rgu34a and rtu34 chips using
> ‘combineAffyBatch’ from the package matchprobes.  My problem is that the
> resulting AffyBatch object has array sizes of 0x0. I am running version
> 2.1.0 of R for windows and have version 1.0.22 of matchprobes.
> 
> Here is my code:
> 
> 
> pd1<-new("phenoData",pData=data.frame(id="ny"), varLabels=list("phenovar"))
> pd2<-new("phenoData",pData=data.frame(id="ge"), varLabels=list("phenovar"))
> 
> 
>>x1<-read.affybatch(file1,compress=TRUE, phenoData=pd1)
>>x2<-read.affybatch(file2,compress=TRUE, phenoData=pd2)
> 
> 
> comb<-combineAffyBatch(list(x1,x2),c("rgu34aprobe","rtu34probe"),
> 	"newset",verbose=TRUE)
> 
> package:rgu34aprobe     rgu34aprobe
> package:rtu34probe      rtu34probe
> 16612 unique probes in common
> 
>   Here is what I get
> 
> 
>>comb
> 
> $dat
> AffyBatch object
> size of arrays=0x0 features (523 kb)
> cdf=newset (1036 affyids)
> number of samples=2
> number of genes=1036
> annotation=
> 
> $cdf
> <environment: 074EDC14>
> 
> What can I do to fix this?
> Jared
> 
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> 


-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber